OpenRaiser/Intern-Atlas huggingface dataset:
An Auditable Agent Platform For Automated Molecular Optimisation
Venue: arXiv cs.LG 2025
Year: 2025

Drug discovery frequently loses momentum when data, expertise, and tools are scattered, slowing design cycles. To shorten this loop we built a hierarchical, tool using agent framework that automates molecular optimisation. A Principal Researcher defines each objective, a Database agent retrieves target information, an AI Expert generates de novo scaffolds with a sequence to molecule deep learning model, a Medicinal Chemist edits them while invoking a docking tool, a Ranking agent scores the candidates, and a Scientific Critic polices the logic. Each tool call is summarised and stored causing the full reasoning path to remain inspectable. The agents communicate through concise provenance records that capture molecular lineage, to build auditable, molecule centered reasoning trajectories and reuse successful transformations via in context learning. Three cycle research loops were run against AKT1 protein using five large language models. After ranking the models by mean docking score, we ran 20 independent scale ups on the two top performers. We then compared the leading LLMs' binding affinity results across three configurations, LLM only, single agent, and multi agent. Our results reveal an architectural trade off, the multi agent setting excelled at focused binding optimization, improving average predicted binding affinity by 31%. In contrast, single agent runs generated molecules with superior drug like properties at the cost of less potent binding scores. Unguided LLM runs finished fastest, yet their lack of transparent tool signals left the validity of their reasoning paths unverified. These results show that test time scaling, focused feedback loops and provenance convert general purpose LLMs into auditable systems for molecular design, and suggest that extending the toolset to ADMET and selectivity predictors could push research workflows further along the discovery pipeline.
Neighborhood-Preserving Voronoi Treemaps
Venue: arXiv cs.GR 2025
Year: 2025

Voronoi treemaps are used to depict nodes and their hierarchical relationships simultaneously. However, in addition to the hierarchical structure, data attributes, such as co-occurring features or similarities, frequently exist. Examples include geographical attributes like shared borders between countries or contextualized semantic information such as embedding vectors derived from large language models. In this work, we introduce a Voronoi treemap algorithm that leverages data similarity to generate neighborhood-preserving treemaps. First, we extend the treemap layout pipeline to consider similarity during data preprocessing. We then use a Kuhn-Munkres matching of similarities to centroidal Voronoi tessellation (CVT) cells to create initial Voronoi diagrams with equal cell sizes for each level. Greedy swapping is used to improve the neighborhoods of cells to match the data's similarity further. During optimization, cell areas are iteratively adjusted to their respective sizes while preserving the existing neighborhoods. We demonstrate the practicality of our approach through multiple real-world examples drawn from infographics and linguistics. To quantitatively assess the resulting treemaps, we employ treemap metrics and measure neighborhood preservation.
Toward a Graph-Theoretic Model of Belief: Confidence, Credibility, and Structural Coherence
Venue: arXiv cs.AI 2025
Year: 2025

Belief systems are often treated as globally consistent sets of propositions or as scalar-valued probability distributions. Such representations tend to obscure the internal structure of belief, conflate external credibility with internal coherence, and preclude the modeling of fragmented or contradictory epistemic states. This paper introduces a minimal formalism for belief systems as directed, weighted graphs. In this framework, nodes represent individual beliefs, edges encode epistemic relationships (e.g., support or contradiction), and two distinct functions assign each belief a credibility (reflecting source trust) and a confidence (derived from internal structural support). Unlike classical probabilistic models, our approach does not assume prior coherence or require belief updating. Unlike logical and argumentation-based frameworks, it supports fine-grained structural representation without committing to binary justification status or deductive closure. The model is purely static and deliberately excludes inference or revision procedures. Its aim is to provide a foundational substrate for analyzing the internal organization of belief systems, including coherence conditions, epistemic tensions, and representational limits. By distinguishing belief structure from belief strength, this formalism enables a richer classification of epistemic states than existing probabilistic, logical, or argumentation-based approaches.
Learned Adaptive Indexing
Venue: arXiv cs.DB 2025
Year: 2025

Indexes can significantly improve search performance in relational databases. However, if the query workload changes frequently or new data updates occur continuously, it may not be worthwhile to build a conventional index upfront for query processing. Adaptive indexing is a technique in which an index gets built on the fly as a byproduct of query processing. In recent years, research in database indexing has taken a new direction where machine learning models are employed for the purpose of indexing. These indexes, known as learned indexes, can be more efficient compared to traditional indexes such as B+-tree in terms of memory footprints and query performance. However, a learned index has to be constructed upfront and requires training the model in advance, which becomes a challenge in dynamic situations when workload changes frequently. To the best of our knowledge, no learned indexes exist yet for adaptive indexing. We propose a novel learned approach for adaptive indexing. It is built on the fly as queries are submitted and utilizes learned models for indexing data. To enhance query performance, we employ a query workload prediction technique that makes future workload projection based on past workload data. We have evaluated our learned adaptive indexing approach against existing adaptive indexes for various query workloads. Our results show that our approach performs better than others in most cases, offering 1.2x - 5.6x improvement in query performance.
Semantic-aware Graph-guided Behavior Sequences Generation with Large Language Models for Smart Homes
Venue: arXiv cs.AI 2025
Year: 2025

As smart homes become increasingly prevalent, intelligent models are widely used for tasks such as anomaly detection and behavior prediction. These models are typically trained on static datasets, making them brittle to behavioral drift caused by seasonal changes, lifestyle shifts, or evolving routines. However, collecting new behavior data for retraining is often impractical due to its slow pace, high cost, and privacy concerns. In this paper, we propose SmartGen, an LLM-based framework that synthesizes context-aware user behavior data to support continual adaptation of downstream smart home models. SmartGen consists of four key components. First, we design a Time and Semantic-aware Split module to divide long behavior sequences into manageable, semantically coherent subsequences under dual time-span constraints. Second, we propose Semantic-aware Sequence Compression to reduce input length while preserving representative semantics by clustering behavior mapping in latent space. Third, we introduce Graph-guided Sequence Synthesis, which constructs a behavior relationship graph and encodes frequent transitions into prompts, guiding the LLM to generate data aligned with contextual changes while retaining core behavior patterns. Finally, we design a Two-stage Outlier Filter to identify and remove implausible or semantically inconsistent outputs, aiming to improve the factual coherence and behavioral validity of the generated sequences. Experiments on three real-world datasets demonstrate that SmartGen significantly enhances model performance on anomaly detection and behavior prediction tasks under behavioral drift, with anomaly detection improving by 85.43% and behavior prediction by 70.51% on average. The code is available at https://github.com/horizonsinzqs/SmartGen.
LRQ-DiT: Log-Rotation Post-Training Quantization of Diffusion Transformers for Image and Video Generation
Venue: arXiv cs.CV 2025
Year: 2025

Diffusion Transformers (DiTs) have achieved impressive performance in text-to-image and text-to-video generation. However, their high computational cost and large parameter sizes pose significant challenges for usage in resource-constrained scenarios. Effective compression of models has become a crucial issue that urgently needs to be addressed. Post-training quantization (PTQ) is a promising solution to reduce memory usage and accelerate inference, but existing PTQ methods suffer from severe performance degradation under extreme low-bit settings. After experiments and analysis, we identify two key obstacles to low-bit PTQ for DiTs: (1) the weights of DiT models follow a Gaussian-like distribution with long tails, causing uniform quantization to poorly allocate intervals and leading to significant quantization errors. This issue has been observed in the linear layer weights of different DiT models, which deeply limits the performance. (2) two types of activation outliers in DiT models: (i) Mild Outliers with slightly elevated values, and (ii) Salient Outliers with large magnitudes concentrated in specific channels, which disrupt activation quantization. To address these issues, we propose LRQ-DiT, an efficient and accurate post-training quantization framework for image and video generation. First, we introduce Twin-Log Quantization (TLQ), a log-based method that allocates more quantization intervals to the intermediate dense regions, effectively achieving alignment with the weight distribution and reducing quantization errors. Second, we propose an Adaptive Rotation Scheme (ARS) that dynamically applies Hadamard or outlier-aware rotations based on activation fluctuation, effectively mitigating the impact of both types of outliers. Extensive experiments on various text-to-image and text-to-video DiT models demonstrate that LRQ-DiT preserves high generation quality.
VQA support to Arabic Language Learning Educational Tool
Venue: arXiv cs.AI 2025
Year: 2025

We address the problem of scarcity of educational Arabic Language Learning tools that advocate modern pedagogical models such as active learning which ensures language proficiency. In fact, we investigate the design and evaluation of an AI-powered educational tool designed to enhance Arabic language learning for non-native speakers with beginner-to-intermediate proficiency level. The tool leverages advanced AI models to generate interactive visual quizzes, deploying Visual Question Answering as the primary activity. Adopting a constructivist learning approach, the system encourages active learning through real-life visual quizzes, and image-based questions that focus on improving vocabulary, grammar, and comprehension. The system integrates Vision-Language Pretraining models to generate contextually relevant image description from which Large Language Model generate assignments based on customized Arabic language Learning quizzes thanks to prompting. The effectiveness of the tool is evaluated through a manual annotated benchmark consisting of 1266 real-life visual quizzes, with human participants providing feedback. The results show a suitable accuracy rates, validating the tool's potential to bridge the gap in Arabic language education and highlighting the tool's promise as a reliable, AI-powered resource for Arabic learners, offering personalized and interactive learning experiences.
SLA-MORL: SLA-Aware Multi-Objective Reinforcement Learning for HPC Resource Optimization
Venue: arXiv cs.LG 2025
Year: 2025

Dynamic resource allocation for machine learning workloads in cloud environments remains challenging due to competing objectives of minimizing training time and operational costs while meeting Service Level Agreement (SLA) constraints. Traditional approaches employ static resource allocation or single-objective optimization, leading to either SLA violations or resource waste. We present SLA-MORL, an adaptive multi-objective reinforcement learning framework that intelligently allocates GPU and CPU resources based on user-defined preferences (time, cost, or balanced) while ensuring SLA compliance. Our approach introduces two key innovations: (1) intelligent initialization through historical learning or efficient baseline runs that eliminates cold-start problems, reducing initial exploration overhead by 60%, and (2) dynamic weight adaptation that automatically adjusts optimization priorities based on real-time SLA violation severity, creating a self-correcting system. SLA-MORL constructs a 21-dimensional state representation capturing resource utilization, training progress, and SLA compliance, enabling an actor-critic network to make informed allocation decisions across 9 possible actions. Extensive evaluation on 13 diverse ML workloads using production HPC infrastructure demonstrates that SLA-MORL achieves 67.2% reduction in training time for deadline-critical jobs, 68.8% reduction in costs for budget-constrained workloads, and 73.4% improvement in overall SLA compliance compared to static baselines. By addressing both cold-start inefficiency and dynamic adaptation challenges, SLA-MORL provides a practical solution for cloud resource management that balances performance, cost, and reliability in modern ML training environments.
Understanding the Landscape of Ampere GPU Memory Errors
Venue: arXiv cs.DC 2025
Year: 2025

Graphics Processing Units (GPUs) have become a de facto solution for accelerating high-performance computing (HPC) applications. Understanding their memory error behavior is an essential step toward achieving efficient and reliable HPC systems. In this work, we present a large-scale cross-supercomputer study to characterize GPU memory reliability, covering three supercomputers - Delta, Polaris, and Perlmutter - all equipped with NVIDIA A100 GPUs. We examine error logs spanning 67.77 million GPU device-hours across 10,693 GPUs. We compare error rates and mean-time-between-errors (MTBE) and highlight both shared and distinct error characteristics among these three systems. Based on these observations and analyses, we discuss the implications and lessons learned, focusing on the reliable operation of supercomputers, the choice of checkpointing interval, and the comparison of reliability characteristics with those of previous-generation GPUs. Our characterization study provides valuable insights into fault-tolerant HPC system design and operation, enabling more efficient execution of HPC applications.
Understanding Demand for Shared Autonomous Micro-Mobility
Venue: arXiv cs.ET 2025
Year: 2025

This study examines the behavioral and environmental implications of shared autonomous micro-mobility systems, focusing on autonomous bicycles and their integration with transit in the U.S. While prior research has addressed operational and lifecycle aspects, a critical gap remains in understanding which modes these services are likely to substitute, who is most inclined to adopt them, and how service attributes influence user decisions. We design a context-aware stated preference survey grounded in real-world trips and estimate discrete choice models, including a hybrid model incorporating latent attitudes. Findings indicate that adoption, mode shift, and environmental impacts are highly sensitive to service design. Scenarios with minimal wait and cost yield high adoption but increase emissions, while moderate waits are more likely to reduce impacts. Adoption likelihood varies with demographic characteristics, and outcomes depend on city type, context, and infrastructure assumptions. These insights can inform the development of more sustainable and equitable mobility systems.
MultiRAG: A Knowledge-guided Framework for Mitigating Hallucination in Multi-source Retrieval Augmented Generation
Venue: arXiv cs.IR 2025
Year: 2025

Retrieval Augmented Generation (RAG) has emerged as a promising solution to address hallucination issues in Large Language Models (LLMs). However, the integration of multiple retrieval sources, while potentially more informative, introduces new challenges that can paradoxically exacerbate hallucination problems. These challenges manifest primarily in two aspects: the sparse distribution of multi-source data that hinders the capture of logical relationships and the inherent inconsistencies among different sources that lead to information conflicts. To address these challenges, we propose MultiRAG, a novel framework designed to mitigate hallucination in multi-source retrieval-augmented generation through knowledge-guided approaches. Our framework introduces two key innovations: (1) a knowledge construction module that employs multi-source line graphs to efficiently aggregate logical relationships across different knowledge sources, effectively addressing the sparse data distribution issue; and (2) a sophisticated retrieval module that implements a multi-level confidence calculation mechanism, performing both graph-level and node-level assessments to identify and eliminate unreliable information nodes, thereby reducing hallucinations caused by inter-source inconsistencies. Extensive experiments on four multi-domain query datasets and two multi-hop QA datasets demonstrate that MultiRAG significantly enhances the reliability and efficiency of knowledge retrieval in complex multi-source scenarios. \textcolor{blue}{Our code is available in https://github.com/wuwenlong123/MultiRAG.
PyLate: Flexible Training and Retrieval for Late Interaction Models
Venue: arXiv cs.IR 2025
Year: 2025

Neural ranking has become a cornerstone of modern information retrieval. While single vector search remains the dominant paradigm, it suffers from the shortcoming of compressing all the information into a single vector. This compression leads to notable performance degradation in out-of-domain, long-context, and reasoning-intensive retrieval tasks. Multi-vector approaches pioneered by ColBERT aim to address these limitations by preserving individual token embeddings and computing similarity via the MaxSim operator. This architecture has demonstrated superior empirical advantages, including enhanced out-of-domain generalization, long-context handling, and performance in complex retrieval scenarios. Despite these compelling empirical results and clear theoretical advantages, the practical adoption and public availability of late interaction models remain low compared to their single-vector counterparts, primarily due to a lack of accessible and modular tools for training and experimenting with such models. To bridge this gap, we introduce PyLate, a streamlined library built on top of Sentence Transformers to support multi-vector architectures natively, inheriting its efficient training, advanced logging, and automated model card generation while requiring minimal code changes to code templates users are already familiar with. By offering multi-vector-specific features such as efficient indexes, PyLate aims to accelerate research and real-world application of late interaction models, thereby unlocking their full potential in modern IR systems. Finally, PyLate has already enabled the development of state-of-the-art models, including GTE-ModernColBERT and Reason-ModernColBERT, demonstrating its practical utility for both research and production environments.
VRPRM: Process Reward Modeling via Visual Reasoning
Venue: arXiv cs.LG 2025
Year: 2025

Process Reward Model (PRM) is widely used in the post-training of Large Language Model (LLM) because it can perform fine-grained evaluation of the reasoning steps of generated content. However, most PRMs lack long-term reasoning and deep thinking capabilities. On the other hand, although a few works have tried to introduce Chain-of-Thought capability into PRMs, the annotation cost of CoT-PRM data is too expensive to play a stable role in various tasks. To address the above challenges, we propose VRPRM, a process reward model via visual reasoning, and design an efficient two-stage training strategy. Experimental results show that using only 3.6K CoT-PRM SFT data and 50K non-CoT PRM RL training data, VRPRM can surpass the non-thinking PRM with a total data volume of 400K and achieved a relative performance improvement of up to 118\% over the base model in the BoN experiment. This result confirms that the proposed combined training strategy can achieve higher quality reasoning capabilities at a lower data annotation cost, thus providing a new paradigm for PRM training with more efficient data utilization.
A Scalable Machine Learning Pipeline for Building Footprint Detection in Historical Maps
Venue: arXiv cs.CV 2025
Year: 2025

Historical maps offer a valuable lens through which to study past landscapes and settlement patterns. While prior research has leveraged machine learning based techniques to extract building footprints from historical maps, such approaches have largely focused on urban areas and tend to be computationally intensive. This presents a challenge for research questions requiring analysis across extensive rural regions, such as verifying historical census data or locating abandoned settlements. In this paper, this limitation is addressed by proposing a scalable and efficient pipeline tailored to rural maps with sparse building distributions. The method described employs a hierarchical machine learning based approach: convolutional neural network (CNN) classifiers are first used to progressively filter out map sections unlikely to contain buildings, significantly reducing the area requiring detailed analysis. The remaining high probability sections are then processed using CNN segmentation algorithms to extract building features. The pipeline is validated using test sections from the Ordnance Survey Ireland historical 25 inch map series and 6 inch map series, demonstrating both high performance and improved efficiency compared to conventional segmentation-only approaches. Application of the technique to both map series, covering the same geographic region, highlights its potential for historical and archaeological discovery. Notably, the pipeline identified a settlement of approximately 22 buildings in Tully, Co. Galway, present in the 6 inch map, produced in 1839, but absent from the 25 inch map, produced in 1899, suggesting it may have been abandoned during the Great Famine period.
In-Memory Non-Binary LDPC Decoding
Venue: arXiv cs.DC 2025
Year: 2025

Low-density parity-check (LDPC) codes are an important feature of several communication and storage applications, offering a flexible and effective method for error correction. These codes are computationally complex and require the exploitation of parallel processing to meet real-time constraints. As advancements in arithmetic and logic unit technology allowed for higher performance of computing systems, memory technology has not kept the same pace of development, creating a data movement bottleneck and affecting parallel processing systems more dramatically. To alleviate the severity of this bottleneck, several solutions have been proposed, namely the processing in-memory (PiM) paradigm that involves the design of compute units to where (or near) the data is stored, utilizing thousands of low-complexity processing units to perform out bit-wise and simple arithmetic operations. This paper presents a novel efficient solution for near-memory non-binary LDPC decoders in the UPMEM system, for the best of our knowledge the first real hardware PiM-based non-binary LDPC decoder that is benchmarked against low-power GPU parallel solutions highly optimized for throughput performance. PiM-based non-binary LDPC decoders can achieve 76 Mbit/s of decoding throughput, which is even competitive when compared against implementations running in edge GPUs.